Can you concatenate fastq.gz (zipped) and fastq (non-zipped) files?
Is is possible to concatenate fastq files which are compressed to different degrees (compression using different methods)? Or concatenate a mix of fastq and fastq.gz files?
The following command seems to work (but I cannot tell if the final files are properly compressed or combined)
cat file1.fastq.gz file2.fastq > combined.fastq.gz
• 1,315 views
•
link
updated
by
Pierre Lindenbaum
•
written
by
Eliveri •
•
written
by
Eliveri •
1 answer
but I cannot tell if the final files are properly compressed or combined
gunzip -t combined.fastq.gz && echo "OK"
but I can tell you it's not properly compressed
• 0 views
•
link
written
by
Pierre Lindenbaum
Log in to answer this question.
More posts like this
-
merge vcf.gz file
written by Mali •
-
Converting Bam file to Fasta (Zipped)
written by Eliveri •
-
concatenate 24 stranded specific RNA seq fastq libraries in linux ?
written by slin023 •
-
gzip: merged.fastq.gz not in gzip format
written by Kai_Qi
-
IF statement (in linux script) to merge Fastq files with similar (but not the same) names
written by endretoth •
-
How to concatenate RNA-seq files generated in differnt lanes
written by desu_gett •
-
Merge FastQ Files
written by shounak.chakraborty1990 •
-
BWA mem output inconsistent on same but re-ordered FASTQ input
written by ramy •
-
bash for loop with two type of files
written by mbk0asis
-
Tophat Error: It Tries To Execute Lines In Fastq Files
written by newDNASeqer
Even if that works you probably don't want to play with fire. Either uncompress the first file and then cat/bgzip or bgzip the second file and then cat. Tools may fail silently if they have trouble with files created the way you are showing above.